In many sequencing by synthesis (SBS) systems, clonal amplification and SBS are performed in glass flow cell channels. PCR primers are attached to the inner surface of the channels via a passively bound polymer coating. Weakly bound polymer chains are washed away prior to use, but the remaining polymer can become depleted to varying extents during extensive cycles of SBS, causing progressive loss of signal. This is a particular concern when high pH and elevated temperature conditions are employed.